Targeting MYC Transcription with Small Peptide Derived from KSHV Transactivator (RNA-Seq)

Herpesviruses rely on host cell transcription and translation machineries for replication. Viral proteins thus function to redirect multiple cellular proteins for viral replication. In herpesvirus replicating cells, host cell gene transcription is frequently down-regulated because important transcriptional apparatuses are appropriated by viral transcription factors. Here we show that an evolutionally-shaped viral protein sequence is a great starting material for unique drug development to modulate cellular transcription. Cellular c-Myc protein (MYC) is overexpressed in over 70% of all types of cancer cells and therefore a very attractive target to control cancer cell growth. We identified a small functional peptide derived from the Kaposi's sarcoma-associated herpesvirus transactivator (K-Rta), which strongly attenuates MYC expression, reduces cell proliferation, and selectively kills cancer cells in both tissue culture and a xenograft tumor mouse model. Mechanistically, the peptide blocks promoter-enhancer interactions by preventing coactivator complex consisting of Nuclear receptor coactivator 2, p300, and SWI/SNF proteins from engaging the MYC promoter in leukemia cells. Target gene profiling with SLAM-seq suggests that the viral peptide attenuates MYC expression through a mechanism likely different from that of BET bromodomain inhibitors. Furthermore, fusing the 13 amino acids peptide with humanized anti-CD22 single chain armed the antibody drug with cell killing ability, and inhibited cell growth in soft agar. Our studies thus demonstrate the utility of the peptide sequence as a therapeutics module, which may be used to modulate MYC activity in a cell type-specific manner. The goal of these studies was to utilize comprehensive transcriptomic profiling in order to determine the gene expression and pathway alterations mediated by treatment with a novel small functional peptide therapeutic derived from the Kaposi's sarcoma-associated herpesvirus (KSHV)-transactivator (K-Rta), which strongly attenuates MYC expression. This was performed in the context of the (TREx)BCBL-1, BC-1, and BC-3 cell line models, which are derived from KSHV-infected human primary effusion lymphomas (PEL) and contain latent KSHV genomes. TREx-K-Rta BCBL-1, also referred to as (TREx)BCBL-1, is an engineered subline, which contains a Tetracycline/Doxycycline (Dox)-inducible Flagx3- and HAx3-tagged K-Rta expression cassette. Viral reactivation is then stimulated by inducing K-Rta expression in individual TREx-K-Rta BCBL-1 cultures by treatment with Dox for 24 hours. For this study, replicate cultures from each cell line were treated with either wild-type or mutant versions of the petide at a concentration of 24uM for 24hrs. Following treatment, the cells were then harvested for isolation of total RNA and followed by library preparation and next-generation sequencing (NGS). UPDATE: [Feb 27, 2024] The raw data associated with GSM5284906 and GSM5284909 were corrected.